<b><i>Introduction:</i></b> Relative risk, risk factors, clinical presentation, onset of symptoms, and age at diagnosis differ between arterial ischaemic stroke (AIS) and cerebral sinovenous thrombosis (CSVT) in neonates. Distinguishing these 2 entities in time clinically can be of eminent importance. <b><i>Methods:</i></b> Active surveillance for AIS and CSVT was performed in 345 German paediatric hospitals. Only cases confirmed by cerebral MRI were included in our analysis. Patients with AIS were compared to CSVT cases with regard to age at diagnosis, pattern of clinical symptoms, and risk factors. <b><i>Results:</i></b> Data on 144 AIS and 51 CSVT neonatal cases were collected from 2015 to 2017. The relative risk of AIS was 2.8 (95% CI 2.1; 3.9) times higher than that of CSVT. CSVT patients were more likely to be born premature (CSVT 14/48, 29.2%; AIS 19/140, 13.2%; <i>p</i> = 0.02) and to have signs of perinatal acidosis (e.g., umbilical artery pH ≤ 7.1 30.2% CSVT vs. 13.5% AIS <i>p</i> = 0.01). Generalized seizures and lethargy were more likely to occur in infants with CSVT (<i>p</i> < 0.0001). Age at onset of symptoms and at time of diagnoses was shifted to older ages in CSVT (<i>p</i> < 0.0001). <b><i>Discussion/Conclusion:</i></b> The risk for AIS is about 3 times higher than that for CSVT in neonates. A higher proportion of critically ill infants in CSVT and a later onset of symptoms may indicate that perinatal and postnatal risk factors are more important for CSVT than for AIS. The data underline the need for an increased awareness of CSVT in critically ill infants.